rs2388376

Variant names:

• chr13-29985289-G-C
• rs2388376
• ENST00000725508.1:n.523+3474G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000725508.1(ENSG00000294728):​n.523+3474G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0529 in 152,148 control chromosomes in the GnomAD database, including 290 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.053 (290 hom., cov: 32)
• Consequence: ENSG00000294728 ENST00000725508.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261
• Publications: 5 publications found

Genes affected

ENSG00000294728 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294728	ENST00000725508.1	n.523+3474G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0529 AC: 8042 AN: 152030 Hom.: 289 Cov.: 32

Gnomad AFR AF: 0.0216

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.0509

Gnomad FIN AF: 0.0509

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0523

Gnomad OTH AF: 0.0556

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0529 AC: 8043 AN: 152148 Hom.: 290 Cov.: 32 AF XY: 0.0549 AC XY: 4080 AN XY: 74374

African (AFR) AF: 0.0215 AC: 894 AN: 41514

American (AMR) AF: 0.124 AC: 1890 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0271 AC: 94 AN: 3468

East Asian (EAS) AF: 0.130 AC: 674 AN: 5180

South Asian (SAS) AF: 0.0514 AC: 247 AN: 4808

European-Finnish (FIN) AF: 0.0509 AC: 538 AN: 10578

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0523 AC: 3556 AN: 68004

Other (OTH) AF: 0.0546 AC: 115 AN: 2108

Alfa AF: 0.0606 Hom.: 42

Bravo AF: 0.0583

Asia WGS AF: 0.0890 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.47
PhyloP100		0.26

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2388376; hg19: chr13-30559426;